Genome of South African dwarf chameleons decoded

Genome of South African dwarf chameleons decoded

by Alex Negro Science

After a reference genome for the panther chameleon (Furcifer pardalis) was recently published for the first time in China, scientists from South Africa have now followed with the genome of two dwarf chameleon species.

For the analyses, a male Bradypodion pumilum from Cape Town and a male Bradypodion ventrale from an introduced population in Johannesburg were taken. Muscle and liver tissue was used for long sequencing (HiC). The genome size of Bradypodion pumilum is 2.43 gigabase pairs (Gb), that of Bradypodion ventrale 2.40 Gb. The BUSCO analysis demonstrated a high completeness with about 97% of all existing coding genes in vertebrates. Furthermore, the current publication confirms the six macrochromosomes already found from the karyotype in Bradypodion thamnobates 2017. Various comparisons with Anolis sagrei were made. It remains open which chromosomes in Bradypodion are sex chromosomes.

The genomes can be viewed in the NCBI BioProject under the number PRJNA9861319 and under the BioSample numbers SAMN35825189 and SAMN35825190 respectively.

De novo whole genome assemblies for two Southern African Dwarf Chameleons (Bradypodion, Chamaeleonidae)
Jody M. Taft, Krystal A. Tolley, Graham J. Alexander, Anthony J. Geneva
Genome Biology and Evolution 15 (10), 2023, pp. 1-8
DOI: 10.1093/gbe/evad182

Genome of the panther chameleon decoded

Genome of the panther chameleon decoded

by Alex Negro Science

In recent decades, genetic research has developed rapidly. Since 2009, the so-called high fidelity (HiFi) Pacbio sequencing method has been available for sequencing genomes. Nevertheless, relatively little is being done in the reptile field. There are only about a hundred so-called reference genomes for reptiles, and none at all for chameleons. Scientists from China have now published a reference genome for the panther chameleon (Furcifer pardalis).

For the analysis, a 5-year-old male captive panther chameleon was killed using isoflurane and then dissected. Different tissues were frozen in liquid nitrogen. Skeletal muscle was used for short genome DNA sequencing and HI-C sequencing. Liver was used for HiFi sequencing. RNA from heart, liver, spleen, testis, lung, kidney, and skin were used for transcriptome sequencing.

The genome size of the panther chameleon from the K-mer analysis is 1.61 gigabase pairs (Gbp), containing only 22 so-called contigs, sets of overlapping DNA. The karyotype contains 11 chromosomes, each consisting of one to four contigs. Ten out of eleven chromosomes have repeat sequences (TAACCC). BUSCO analysis demonstrated a high completeness of the genome. The genome can be viewed in the NCBI BioProject under the number PRJNA974816 and in ScienceDataBank.

Efficient and highly continuous chromosome-level genome assembly of the first chameleon genome
Hongxin Xie, Zixuan Chen, Shuai Pang, Weiguo Du
Genome Biology and Evolution 131, 2023
DOI: 10.1093/gbe/evad131

 

Picture: Alex Laube

Minimally invasive methods for obtaining DNA samples from chameleons

Minimally invasive methods for obtaining DNA samples from chameleons

by Alex Negro Tiermedizin Science

To reliably identify or compare chameleon species, genetic samples of the animals concerned are necessary. Traditionally, scientists have used organ or muscle samples from euthanized chameleons in museum collections or – less commonly – cut tail tips or blood samples from living chameleons. Researchers at the American College in Athens, Greece, have studied whether more minimally invasive methods would also be a good alternative.

They sampled 23 Chamaeleo africanus in the area of the lagoon of Pylos (Divari wetland between Gialova and the bay of Voidokilia) in the Peloponnese in Greece using buccal swabs. This involves running a sterile swab on the inside of the cheek through the chameleon’s mouth for six seconds. Blood was taken from the ventral tail vein of eight other Chamaeleo africanus for comparison. Sampling took less than a minute. Afterward, the chameleons were returned to where they were found. The swabs were transported refrigerated in a special buffer solution in Eppendorf cups and then frozen.

In the laboratory, the researchers were able to extract both nuclear and mitochondrial DNA from all the swabs. However, the quantity and quality of the DNA extracted were lower than in the blood samples. For most applications such as PCR amplification and gene sequencing, however, the scientists said the quantity was sufficient. In terms of invasiveness and destructiveness, buccal swabbing is certainly preferable to killing or injuring individual chameleons. Studies on other reptiles suggest that rapid freezing is not mandatory either – in the field, a functioning cool chain could become a problem in many chameleons’ countries of origin. The current study advises against ethanol as a fixing solution; the buffer solutions used lead to better results.

Buccal swabbing appears to be less applicable for cases where additional material for future studies might be preserved, for example when describing new species, or when sequencing the entire genome. However, the method is certainly a good alternative, especially for particularly small chameleon populations where lethal sampling could already significantly limit the breeding pool.

Buccal swabs as an effective alternative to traditional tissue sampling methods for DNA analyses in Chamaeleonidae
Maria Koutsokali, Christina Dianni and Michael Valahas
Wildlife Biology
DOI: 10.1002/wlb3.01052